Move dumps related to datasets to one place

* examples/dump-dataset-metadata.scm: Add dump-gene-chip,
dump-publishfreeze, dump-genofreeze, dump-probesetfreeze
* examples/dump-genotype.scm: Delete dump-genofreeze.
* examples/dump-phenotype.scm: Delete dump-publishfreeze.
* examples/dump-probesetfreeze.scm: Delete file

4 files changed, 140 insertions, 194 deletions

diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index e732772..8f381b7 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -56,6 +56,37 @@
     (set v:postal-code (field Investigators ZipCode))
     (set v:country-name (field Investigators Country))))
 
+(define-dump dump-gene-chip
+  (tables (GeneChip
+           (left-join Species "USING (SpeciesId)")))
+  (schema-triples
+   (gnc:geneChip a skos:Concept)
+   (gnc:geneChip
+    skos:description
+    "This is a set of controlled terms that are used to describe a given gene chip/platform")
+   (gnt:hasGeoSeriesId rdfs:domain gnc:platform)
+   (gnt:belongsToSpecies a owl:ObjectProperty)
+   (gnt:belongsToSpecies skos:definition "This resource belongs to this given species")
+   (gnt:belongsToSpecies rdfs:domain gnc:geneChip)
+   (gnt:hasGeoSeriesId rdfs:domain gnc:geneChip)
+   (gnt:hasGOTreeValue a owl:ObjectProperty)
+   (gnt:hasGOTreeValue skos:definition "This resource the following GO tree value")
+   (gnt:hasGOTreeValue rdfs:domain gnc:geneChip))
+  (triples (string->identifier "platform" (field GeneChip Name))
+    (set rdf:type 'gnc:geneChip)
+    (set rdfs:label (field GeneChip GeneChipName))
+    (set skos:prefLabel (field GeneChip Name))
+    (set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
+                               Title)))
+    (set gnt:hasGOTreeValue (field GeneChip Go_tree_value))
+    (set gnt:belongsToSpecies
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))
+    (set gnt:hasGeoSeriesId
+         (ontology 'geoSeries:
+                   (string-trim-both (field GeneChip GeoPlatform))))))
+
 (define-dump dump-info-files
   (tables (InfoFiles
            (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name")
@@ -219,6 +250,109 @@
     (set gnt:hasAcknowledgement (sanitize-rdf-string
                                  (field Datasets Acknowledgment)))))
 
+;; These are phenotype datasets that don't have Infofile metadata
+(define-dump dump-publishfreeze
+  (tables (PublishFreeze
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
+           (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
+          "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL")
+  (triples
+      (string->identifier
+       ""
+       (regexp-substitute/global #f "[^A-Za-z0-9:]"
+                                 (field PublishFreeze Name)
+                                 'pre "_" 'post)
+       #:separator ""
+       #:proc string-capitalize-first)
+    (set rdf:type 'gnc:phenotypeDataset)
+    (set rdfs:label (field PublishFreeze Name))
+    (set skos:prefLabel (field PublishFreeze FullName))
+    (set skos:altLabel (field PublishFreeze ShortName))
+    (set dct:created (annotate-field
+                      (field PublishFreeze CreateTime)
+                      '^^xsd:date))
+    (set gnt:belongsToSet
+         (string->identifier
+          "inbredSet" (field InbredSet Name)
+          #:separator ""
+          #:proc string-capitalize-first))))
+
+(define-dump dump-genofreeze
+  (tables (GenoFreeze
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
+           (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
+          "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
+  (triples
+      (string->identifier
+       ""
+       (regexp-substitute/global
+        #f "[^A-Za-z0-9:]"
+        (regexp-substitute/global
+         #f "[^A-Za-z0-9:]"
+         (field GenoFreeze Name)
+         'pre "_" 'post)
+        'pre "_" 'post)
+       #:separator ""
+       #:proc string-capitalize-first)
+    (set rdf:type 'gnc:genotypeDataset)
+    (set rdfs:label (field GenoFreeze Name))
+    (set skos:prefLabel (field GenoFreeze FullName))
+    (set skos:altLabel (field GenoFreeze ShortName))
+    (set dct:created (annotate-field
+                      (field GenoFreeze CreateTime)
+                      '^^xsd:date))
+    (set gnt:belongsToSet
+         (string->identifier
+            "inbredSet" (field InbredSet Name)
+            #:separator ""
+            #:proc string-capitalize-first))))
+
+;; Molecular Traits are also referred to as ProbeSets
+(define-dump dump-probesetfreeze
+  (tables (ProbeSetFreeze
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
+           (left-join ProbeFreeze "USING (ProbeFreezeId)")
+           (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
+           (left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
+           (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
+          "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
+  (schema-triples
+   (gnt:usesNormalization rdfs:domain gnc:probeset)
+   (gnt:usesDataScale rdfs:domain gnc:probeset)
+   (gnt:usesDataScale a owl:ObjectProperty)
+   (gnt:usesDataScale skos:definition "Thi data scale this resource uses"))
+  (triples
+      (string->identifier
+       ""
+       (regexp-substitute/global
+        #f "[^A-Za-z0-9:]"
+        (field ProbeSetFreeze Name)
+        'pre "_" 'post)
+       #:separator ""
+       #:proc string-capitalize-first)
+    (set rdf:type 'gnc:probesetDataset)
+    (set gnt:usesNormalization
+         (string->identifier "avgmethod"
+                             ;; If AvgMethodName is NULL, assume N/A.
+                             (if (string-blank? (field AvgMethod Name AvgMethodName))
+                                 "N/A" (field AvgMethod Name AvgMethodName))))
+    (set dct:title (field ProbeSetFreeze FullName))
+    (set rdfs:label (field ProbeSetFreeze ShortName))
+    (set skos:prefLabel (field ProbeSetFreeze Name))
+    (set skos:altLabel (field ProbeSetFreeze Name2))
+    (set dct:created (annotate-field
+                      (field ProbeSetFreeze CreateTime)
+                      '^^xsd:datetime))
+    (set gnt:usesDataScale (field ProbeSetFreeze DataScale))
+    (set gnt:hasTissue
+         (string->identifier
+          "tissue"
+          (field Tissue Short_Name)))
+    (set gnt:belongsToSet
+         (string->identifier
+          "inbredSet" (field InbredSet Name)
+          #:separator ""
+          #:proc string-capitalize-first))))
 
 
 
@@ -242,7 +376,11 @@
     ("dct:" "<http://purl.org/dc/terms/>")))
  (inputs
   (list dump-info-files
-        dump-investigators))
+        dump-publishfreeze
+        dump-genofreeze
+        dump-probesetfreeze
+        dump-investigators
+        dump-gene-chip))
  (outputs
   '(#:documentation "./docs/dump-info-pages.md"
     #:rdf "/export/data/genenetwork-virtuoso/dump-info-pages.ttl")))
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 04f1af0..30e7796 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -30,37 +30,6 @@
     ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
     [str str]))
 
-(define-dump dump-genofreeze
-  (tables (GenoFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
-           (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
-          "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global
-        #f "[^A-Za-z0-9:]"
-        (regexp-substitute/global
-         #f "[^A-Za-z0-9:]"
-         (field GenoFreeze Name)
-         'pre "_" 'post)
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:genotypeDataset)
-    (set rdfs:label (field GenoFreeze Name))
-    (set skos:prefLabel (field GenoFreeze FullName))
-    (set skos:altLabel (field GenoFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field GenoFreeze CreateTime)
-                      '^^xsd:date))
-    (set gnt:belongsToSet
-         (string->identifier
-            "inbredSet" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first))))
-
-
 (define-dump dump-genotypes
   (tables (Geno
            (left-join Species "USING (SpeciesId)")))
@@ -149,8 +118,7 @@
     ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
     ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
  (inputs
-  (list dump-genofreeze
-        dump-genotypes))
+  (list dump-genotypes))
  (outputs
   '(#:documentation "./docs/dump-genotype.md"
     #:rdf "/export/data/genenetwork-virtuoso/dump-genotype.ttl")))
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
index f5a8c3c..6c52ebb 100755
--- a/examples/dump-phenotype.scm
+++ b/examples/dump-phenotype.scm
@@ -19,34 +19,6 @@
     read))
 
 
-
-;; These are phenotype datasets that don't have Infofile metadata
-(define-dump dump-publishfreeze
-  (tables (PublishFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
-           (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
-          "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL")
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                 (field PublishFreeze Name)
-                                 'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:phenotypeDataset)
-    (set rdfs:label (field PublishFreeze Name))
-    (set skos:prefLabel (field PublishFreeze FullName))
-    (set skos:altLabel (field PublishFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field PublishFreeze CreateTime)
-                      '^^xsd:date))
-    (set gnt:belongsToSet
-         (string->identifier
-            "inbredSet" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first))))
-
 (define-dump dump-phenotypes
   (tables (PublishXRef
            (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
@@ -147,7 +119,6 @@
     ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
  (inputs
   (list
-   dump-publishfreeze
    dump-phenotypes))
  (outputs
   '(#:documentation "./docs/dump-phenotype.md"
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
deleted file mode 100755
index 50307bf..0000000
--- a/examples/dump-probesetfreeze.scm
+++ /dev/null
@@ -1,131 +0,0 @@
-#! /usr/bin/env guile
-!#
-
-(use-modules (srfi srfi-1)
-             (srfi srfi-26)
-             (ice-9 match)
-             (ice-9 regex)
-             (dump strings)
-             (dump sql)
-             (dump triples)
-             (dump special-forms))
-
-
-
-(define %connection-settings
-  (call-with-input-file (list-ref (command-line) 1)
-    read))
-
-
-(define (remap-species-identifiers str)
-  "This procedure remaps identifiers to standard binominal. Obviously this should
-   be sorted by correcting the database!"
-  (match str
-    ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
-    ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
-    ["Macaca mulatta" "Macaca nemestrina"]
-    ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
-    [str str]))
-
-
-(define-dump dump-gene-chip
-  (tables (GeneChip
-           (left-join Species "USING (SpeciesId)")))
-  (schema-triples
-   (gnc:geneChip a skos:Concept)
-   (gnc:geneChip
-    skos:description
-    "This is a set of controlled terms that are used to describe a given gene chip/platform")
-   (gnt:hasGeoSeriesId rdfs:domain gnc:platform)
-   (gnt:belongsToSpecies a owl:ObjectProperty)
-   (gnt:belongsToSpecies skos:definition "This resource belongs to this given species")
-   (gnt:belongsToSpecies rdfs:domain gnc:geneChip)
-   (gnt:hasGeoSeriesId rdfs:domain gnc:geneChip)
-   (gnt:hasGOTreeValue a owl:ObjectProperty)
-   (gnt:hasGOTreeValue skos:definition "This resource the following GO tree value")
-   (gnt:hasGOTreeValue rdfs:domain gnc:geneChip))
-  (triples (string->identifier "platform" (field GeneChip Name))
-    (set rdf:type 'gnc:geneChip)
-    (set rdfs:label (field GeneChip GeneChipName))
-    (set skos:prefLabel (field GeneChip Name))
-    (set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
-                               Title)))
-    (set gnt:hasGOTreeValue (field GeneChip Go_tree_value))
-    (set gnt:belongsToSpecies
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                             #:separator ""
-                             #:proc string-capitalize-first))
-    (set gnt:hasGeoSeriesId
-         (ontology 'geoSeries:
-                   (string-trim-both (field GeneChip GeoPlatform))))))
-
-;; Molecular Traits are also referred to as ProbeSets
-(define-dump dump-probesetfreeze
-  (tables (ProbeSetFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
-           (left-join ProbeFreeze "USING (ProbeFreezeId)")
-           (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
-           (left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
-           (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
-          "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
-  (schema-triples
-   (gnt:usesNormalization rdfs:domain gnc:probeset)
-   (gnt:usesDataScale rdfs:domain gnc:probeset)
-   (gnt:usesDataScale a owl:ObjectProperty)
-   (gnt:usesDataScale skos:definition "Thi data scale this resource uses"))
-  (triples
-      (string->identifier
-       ""
-       (regexp-substitute/global
-        #f "[^A-Za-z0-9:]"
-        (field ProbeSetFreeze Name)
-        'pre "_" 'post)
-       #:separator ""
-       #:proc string-capitalize-first)
-    (set rdf:type 'gnc:probesetDataset)
-    (set gnt:usesNormalization
-         (string->identifier "avgmethod"
-                             ;; If AvgMethodName is NULL, assume N/A.
-                             (if (string-blank? (field AvgMethod Name AvgMethodName))
-                                 "N/A" (field AvgMethod Name AvgMethodName))))
-    (set dct:title (field ProbeSetFreeze FullName))
-    (set rdfs:label (field ProbeSetFreeze ShortName))
-    (set skos:prefLabel (field ProbeSetFreeze Name))
-    (set skos:altLabel (field ProbeSetFreeze Name2))
-    (set dct:created (annotate-field
-                      (field ProbeSetFreeze CreateTime)
-                      '^^xsd:datetime))
-    (set gnt:usesDataScale (field ProbeSetFreeze DataScale))
-    (set gnt:hasTissue
-         (string->identifier
-          "tissue"
-          (field Tissue Short_Name)))
-    (set gnt:belongsToSet
-         (string->identifier
-            "inbredSet" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first))))
-
-
-
-(dump-with-documentation
- (name "Probeset freeze metadata")
- (connection %connection-settings)
- (table-metadata? #f)
- (prefixes
-  '(("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
-    ("gn:" "<http://genenetwork.org/id/>")
-    ("gnc:" "<http://genenetwork.org/category/>")
-    ("dct:" "<http://purl.org/dc/terms/>")
-    ("owl:" "<http://www.w3.org/2002/07/owl#>")
-    ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
-    ("gnt:" "<http://genenetwork.org/term/>")
-    ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
-    ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
-    ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
- (inputs
-  (list dump-gene-chip
-        dump-probesetfreeze))
- (outputs
-  '(#:documentation "./docs/dump-gene-chip.md"
-    #:rdf "./verified-data/dump-probesetfreeze.ttl")))